Nextflow基本使用

Nextflow官方文档：Get started — Nextflow 21.10.0 documentation

nextflow-io/nextflow: A DSL for data-driven computational pipelines (github.com)

安装Nextflow

conda安装nextflow就好了

conda install -y nextflow

第一次使用

把下面代码放入tutorial.nf

#!/usr/bin/env nextflow

params.str = 'Hello world!'

process splitLetters {

    output:
    file 'chunk_*' into letters

    """
    printf '${params.str}' | split -b 6 - chunk_
    """
}


process convertToUpper {

    input:
    file x from letters.flatten()

    output:
    stdout result

    """
    cat $x | tr '[a-z]' '[A-Z]'
    """
}

result.view { it.trim() }

nextflow run tutorial.nf

Process

process sayHello {

    """
    echo 'Hello world!' > file
    """

}

使用nf-core

Pipelines » nf-core

nextflow run nf-core/rnaseq